GgaINT0126306 @ galGal4
Intron Retention
Gene
ENSGALG00000000936 | LMX1B
Description
LIM/homeobox protein LMX-1.2 [Source:RefSeq peptide;Acc:NP_990689]
Coordinates
chr17:10150569-10152878:+
Coord C1 exon
chr17:10150569-10150730
Coord A exon
chr17:10150731-10152472
Coord C2 exon
chr17:10152473-10152878
Length
1742 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TGTATACATTTCATTTGCAGGAA
3' ss Score
9.7
Exon sequences
Seq C1 exon
AAGTAATGTCTAACCGAATGGAAGGAATGATGACATCTTACACACCACTTGCACCACCGCAGCAGCAGATTGTAGCAATGGATCAAAGCAGTTATGGCACAGACCCATTTCAGCAGGGTCTGACCCCTCCACAAATGCCAGGCGACCACATGAACCCTTATG
Seq A exon
GTAAGGCATGCATCATTCTGCCGCATCAGAAATAGCAGGGTTCGTATGCTGGTTCACACTCCAAAGGTTCAACGGAGTTTCTTGCTGTTATAATATTTTTCTGGGATTTGTACAAAGGAATTTCTACTGGTCAGTTTTGCGTGTATATTTTCGTGTACACATAAAAGGGTAGAAGAGGGCTCTTCCCAGCCTCTGGACACTACTACAGAGTATAGTTTTGATAAATGATAAAGAAAAGCAACATTATCTCTCCAGCTCCACTTTTTTAAATCACTGTCCAAGACTAAAAATAAACAGTGACAAATTTTCTTTACCTTCCTCACAAGTTTTTCCTTTTTCCTAGAAGCTTTGGGAAGATAGTGCCTTGATAAGTGGTCTATTAAAGAGAAGTGATCCATTTATTCAAAAATAAATAACCACCCCTCAAAGATCCCTCAGATCACATGCATGGATTTGTTCTTGAGCTATCGAGAGATATGTCACCACAGGACATTGCTCCTGCATAATGATATTCTCTGTCCAAAATCAAGATGATGGTTTGCTTTTTCAACTTCTTTACCATGCAACATCAAGTGAATAGGTACACTAAATGCTTCACAAGCACATTAAATGCCTAATAATTGATTCTGAACAATTGCAGTGTGGCACTTAAATAAAATTTAAGAGGATTTCTCAGACTGTGACTATTGGCCTTGCCATAGACAAAGAGGACCTGTTTACATCAGACTCTTTTGTGTTGACCGGGAGCACTTCATTGCAGTTACACGTGCACATGACTGCCGTGAGCGTGGATTGCACAAACTAACAAGAAATCTGGCTTGGGTCCGTATGACTGCTTTTTCCTCTGAGGCAAGACCACAGTGCTCGCCAGGCAATTTGGTAAATACTGTAGGGAGCTGAGGATATTTGAAGTGCAAATGAGCATTAGATGACTTGTGATTTTGTTGCTAACAATGTGCTTGGCAATTTCTAAGCAAAACTCCTTTGGAGGCATGTTCTGTGTTCCAAAACCAATGCAGGAATTAAGACAAAGCCATTTTAAATGAATGTGTAAGGAAAAAGAACCAGAGTAACACTTTCCTAAAGCTCACATTACTTGAGCTAGAGCTCTTTCTGGTACCTTAAAATATGAAATAAGCTGAAATTGTAGTTGCTAAGGGAAATAAATGGTGCCGTGTTCCAAACCAGCCCACGAAGAGTGGAATTTTCTGAAAGGAAAGCATATTTACAACTATAGCTCATTTGAGGCCAGGAAAACTGGGCCTCCTCCTGGGCCTGGTTGCCTTTGTCGGCCTGCCTTTTGCTTCGTGTGTAAACCAAGACCATTACTGGTTATGGTGCTCAGGCCACTTTTTTCCACTGTGGGCTCAGTGGTCCTGCATTCCTGCCCTGAGCCCCCACAAGTGCTCAGTGGCAGCTCATGGGGCACCAGGAGCCCTCTTCTCCCCTGACATTGTTTGCTCACGTCATCAGCCAAGGCTTGCTGTTGACTGACGTATATATTTGAAACTGGCAGGCTTCCACATTTCTAAGTGATACTGCTGCCAGCTGAACTCTGTAAATTGGTTGCTAGCCTTTCTTTTTATAGGTCAGACCCTTAGAGCCAAATTACATTAACATGCAAAAGCAAGATCAGAAGCATTCCCTTTTGCTGCAGTGTGCTATATACAAGCATCGCATCCATGTGTACTGTGTCCTCTGGCTGCACAGAATACAGCTTAATGTATACATTTCATTTGCAG
Seq C2 exon
GAAACGACTCCATTTTTCATGATATCGACAGTGATACCTCTTTAACTAGCTTGAGCGACTGTTTTCTTGCCTCTTCTGAAGTTAACTCCATGCAGGCTAGGGTAGGAAACCCCATTGACAGGCTGTACTCTATGCAGAGCTCCTATTTCGCCTCATGAAAATAAACGAAAACAAACAGCCGGCGTGTATTTAGCCAGTGACTTTTTCCGTGCAGCCTCTACAGCCATATGTTGCCCAGCTCTTCCTTCACAGTGACTCCTGCTGCCTCTGGACTGCAAAGAGCATTTTTAGGAAGACTTTATTTGTGTGCATATATGTATGTATGTACGTGCATATATCAGTACCTACCTACCTACATACATACATATATAAACAAAACACATCCACCAGTCACATACCCTTGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000936:ENSGALT00000001376:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.288
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCCATTTCAGCAGGGTCTG
R:
CTCTTTGCAGTCCAGAGGCAG
Band lengths:
343-2085
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]